A. Well, to be perfectly honest, I'm not sure that
he's done research on intelligent design. I'm aware of some of
his published peer reviewed literature and can say that it
concerns a wide variety of topics. I believe nucleotide and
nucleic acid biogenesis, and most recently, a study on random
replacement of neucleoties in genes; in other words, sort of a
moving around of the genetic code and see happens to a gene.

Q. So Dr. Behe has published some peer reviewed
articles, but these are not on intelligent design?

A. To my reading, none of them actually are on
intelligent design. He's published a fair number, good number of
peer reviewed articles in leading peer reviewed scientific
journals, no question.

Q. What is it that Professor Behe brings to the
concept of intelligent design? Does he bring some idea to the
table here?

A. Yes, I think he does. And the idea that he
brings to the table, as you put it, is that the classic argument
from design, which has been around for hundreds, thousands of
years, that biological systems are complex and suggest the
existence of a designer can also be phrased in terms of
biochemistry.

So I believe Dr. Behe's book, Darwin's Black Box,
was subtitled the Biochemical Challenge to Evolution, so what he
brings to the discussion basically is the old argument from
design written up in the new language of biochemistry.

Q. Let's take that in a couple of steps. First of
all, you mentioned Darwin's Black Box. And I direct your
attention to Plaintiff's Exhibit 434. Is this the book to which
you refer?

A. To my understanding, no. Books like this are
subject of what you might call a kind of peer review, which is a
discussion between you and the editor and perhaps the copy
editor, in the same way that my own box, Finding Darwin's God,
was subject to those discussions. But by the standards of
science, neither my book nor Dr. Behe's book counts as a
peer-review publication.

Q. Now you said a moment ago that Dr. Behe's idea
isn't actually new. What do you mean by that?

A. Well, the essential argument that some features
of living things are too complex to have been generated in any
other way other than by attribution to a designer is an idea
that, to my poor understanding of ancient philosophy goes back to
the Greeks. And in western culture, very often one would go back
to a book called
Natural Theology that was written by the
Reverend William Paley
and published, I believe, in 1802.

And Paley's book had what's probably the best
pre-Charles Darwin classical formulation of the idea of
intelligent design. Paley was quite a naturalist. And he really
understood the complexities of living systems, of living organs.
He understood how they work with each other, how delicate the
interplay is. And he said that this very complexity argued for
the presence and the existence of an intelligent designer who
drafted all these organisms and created each of them
individually.

Q. And did Reverend Paley use certain examples
that we might be familiar with?

A. Yes, he did. Paley used a whole variety of
examples. And I believe some of them included the nervous system,
the muscular system, the digestive system. And he used them in a
variety of different types of organisms. So it was a very
interesting book to read, and still is a very interesting book to
read. The example of Paley's that I think is remembered the best
is the example of the eye.

And he pointed out that the eyes that we humans
have -- because among the animal kingdom, we have very good eyes.
Very few animals that can surpass the human eye. Our eye is a
complex multi-part system. And I can't name all the parts not
being an anatomist. But we have the cornea, we have the lens, we
have the iris, we have the aqueous humor, the vitreous humor. We
have the retina in the back of the eye. And for proper vision,
all of these parts have to work together as a coordinated whole.
And that was part of Paley's example.

Paley said, for example, what good would a lens be
without a retina? And what good would a retina be without a lens?
And, therefore, all the parts would have to be assembled
together. And, therefore, only a designer could do that.

Q. So his conclusion was that, there could not be
a natural explanation for this complex system, the eye,
therefore, there was a designer?

A. Well, as far as I can tell, it differs in two
essential respects. The first respect is that, Dr. Behe, although
he praises the arguments of William Paley in several areas of his
book, argues that the argument from design, as Paley's argument
is known, is made most effectively at the level of the cell, at
the level of the molecule.

So he basically has attempted to update Paley's
argument, not by looking at large organ systems, but by looking
at biochemical machines that exist inside individual living
cells. And the second way in which his argument differs from
Paley is that, Dr. Behe, after coming to the same conclusion,
that there had to be an independent designer, a creative force
that created these machines, these pathways, and put them into
being, Dr. Behe is unwillingly to name the identity of that
designer.

And I believe he suggests that the designer, of
course, could be a divine force, but it could be super
intelligent space aliens from Mars or perhaps time traveling cell
biologists going into the past from the future and causing the
structures to be put together.

A. Yes, sir, I have. Dr. Behe and I have discussed
and debated this issue a number of times, and these are examples
that he has used in those discussions.

Q. Now Dr. Behe advances an idea known as
irreducible complexity. Can you explain to us what that idea
consists of?

A. Sure. The idea of irreducible complexity starts
with the observation that living cells contain complex
biochemical systems and machines. They are composed of many
parts. He then suggests that, that complexity is irreducible.
What he means by irreducible complexity is, if we start to take a
few parts away to see if we can make a simpler machine, we very
quickly discover that we can't, that a machine stops
functioning.

Now I've prepared a few demonstratives with quotes
from Dr. Behe's work to sort of illustrate this point, if it's
all right for the Court to show these.

A. So this is, in a way, a summary of Dr. Behe's
argument. And one of the things that I think is important to make
clear to the Court is that, it is absolutely true that there are
many, many structures in the living cell, many biochemical
pathways for which we don't have a detailed biochemical -- excuse
me, a detailed evolutionary explanation. That is a point that all
scientists will concede. Do Doctor --

Q. I'm sorry. Is that true just about evolutionary
theory or is that true about any science?

A. That's true about anything. In cell biology,
for example, I think most people and the court are aware that
when a cell divides, the chromosomes that carry the genetic
information of a cell are moved apart and separated into the two
daughter cells. We have enormous arguments in the field of cell
biology as to what the exact mechanism is by which that force is
generated. We can all see it happen. Any high school student can
watch the separation of chromosomes under a microscope in a high
school laboratory. But we still don't know exactly what the motor
or the mechanism is that moves these apart. There are many, many
other unsolved problems in biology.

A. Sure. So it's important to note that Dr. Behe's
argument does not say simply, well, there are complex structures
within the cell for whom we do not understand the detailed
evolutionary origin of, that's absolutely true. But his argument
really rises to a different level. What I've shown on this slide
is a diagram of the bacterial flagellum.

Now bacteria, of course, are very, very simple
cells. They're found everywhere in nature. They're found, for
example, in our digestive systems. They're found in the skin.
They're found on the surface of the table. Some bacteria have
little whip like structures called flagellum. You might almost
considers them to be outboard motors. And these things whip
around at very high rates of speed, and they propel the bacteria
through water, or sometimes they pull the bacteria in sort of a
screw like motion through the water.

So it's marvelous machines. They are acid powdered
reversible rotary engines. These are marvelous little machines,
and they are made of a whole series of protein parts, some of
which are shown in this little diagram here. Now if we can
animate this slide a little bit. Next point.

Now what I wrote here is that, Dr. Behe has made
very clear in what I think is fairly called his biochemical
argument from design, that that argument depends upon a much
bolder claim than simply saying, scientists have not completely
explained how this structure evolved. And that bolder claim is
shown in the next animated section of this slide.

And that is that, the evolution of complex
biochemical structures cannot even or ever be explained in
principle. And, of course, what he means by that is, there is
some aspect of this complexity, which means we can say not just,
we haven't figured it out yet, but we will never figure it out,
and that's where the evidence for design lies.

Now if I may advance to the next slide. I'll try
to use Dr. Behe's words to explain why he holds this point of
view. The reason that evolution cannot explain, he says, the
origin of such structures is because they have a property, which
he calls irreducible complexity, or they are irreducibly complex.
I thought it best for the Court to read the description of
irreducible complexity in Dr. Behe's own words.

So in the lower part of the the slide, I have a
quotation from page 39 of his book, Darwin's Black Block. And I
will read that to the Court. Quote, By irreducibly complex, I
mean a single system composed of several well-matched,
interacting parts that contribute to the basic function, wherein
the removal of any one of the parts causes the system to
effectively cease functioning.

And now, from my point of view, the key part of
the argument, and I'll continue to read. An irreducibly complex
system cannot be produced directly by slight, successive
modifications of a pre-cursor system -- and that's how evolution
would have to produce it -- because any pre-cursor to an
irreducibly complex system that is missing a part is by
definition non-functional.

So his argument is that, if you have a multi-part
system, and all the parts are necessary to function, you can't
produce that system five parts at a time, six, seven, and
gradually build up the complex system, because there is no
function possible until the last part is snapped into place. And
that's why evolution cannot produce that system.

Now the next slide is another quote of Dr. Behe's
that tries to make this point absolutely explicit as to why you
need the system to be working. He points out, another quote,
Darwin's Black Box, page 39, quote, Since natural selection can
only choose systems that are already working -- and if you
remember, his contention is, if you're missing a part, you're not
working -- then if a biological system cannot be produced
gradually, it would have to arise as an integrated unit, in one
fell swoop, for natural selection to have anything to act upon,
closed quote.

And Dr. Behe rightly points out that, to imagine
such complex systems arising spontaneously in one fell swoop is
something that no serious biologist would argue could happen, and
I will not argue either. So his point is, as long as irreducible
complexity holds, then any system we can identify as irreducibly
complex couldn't have been produced by evolution. It's a very,
very coherent argument.

A. Well, counselor, not so much organisms, but he
certainly identifies some machines and some structures that he
regards as irreducibly complex, one of which, of course, is the
bacterial flagellum. And I pointed out, this slide contains a
diagram of the flagellum. And to the right is actually sort of
what we call a false color, but an electron micrograph showing a
bacterium with several flagellum protruding from one end.

So that is one of the principal systems to which
he points. Now the next slide, please. And I should also point
out, to be a little more responsive than I have been to your
question, that Dr. Behe also says, the blood clotting cascade
that we talked about earlier as an example of an irreducibly
complex system, the eukaryotic cilium, similar system to the
flagellum, that's irreducibly complex, the vesicle targeting
system that parcels out things in living cells, and also the
immune system are all examples of irreducibly complex
systems.

Now what I did in this slide was to prepare a
graphic to make this point as clear as possible to those of us in
court today. And that is to emphasize that complex biochemical
machines composed of multiple interacting parts, if they work,
they can have a function that's favored by natural selection. The
essence of the biochemical argument from irreducible complexity,
however, is that the individual parts of that machine have no
function of their own.

And because they have no function on their own,
they cannot be produced by natural selection and, therefore, the
impediment, the reason you can't get to here from there, you
can't go from individual parts to the machine, is because the
individual parts have no functions of their own.

Now evolutionary biology has grappled with this
problem before. And the next slide shows how evolutionary
biologists generally explain the evolution of complex machines.
And that is, they agree, yes, there are such machines. You need
all these parts for a particular function. But where these
machines come from is, they come from pre-existing machines which
have functions of their own, and that the individual parts of
these machines originate in components that have different
functions.

So the way in which evolutionary biology picks up
Dr. Behe's challenge is to basically say, you're wrong, that the
individual parts of these machines cannot have a function that is
favored by natural selection. Now that, of course, in this slide,
this is not evidence, of course, in the scientific sense. This is
merely an argument.

But the reason I like the way that Dr. Behe has
put his argument, and I like sort of describing it this way, is
because it actually is amenable to a scientific test. Something
that most arguments for intelligent design are not. And the next
slide.

Q. I'm sorry. This is -- is Dr. Behe's argument
for irreducible complexity, is that an argument directly for
design?

A. That's a good point. The answer is, no, it's
not. It really is an argument that says why such systems are not
produceable by evolution. So it's a negative argument against
evolution. It is in itself not evidence. Even if the argument
were correct, it's not evidence of a designer, it's not argument
for design, it simply is an argument that the evolutionary
mechanism wouldn't work in this case.

A. That is correct. As I mentioned earlier, one of
the problems with intelligent design is that it doesn't make any
testable predictions. This actually isn't a testable prediction
of design either. This is simply an argument as to why evolution
wouldn't work. And that can be subjected to a test.

A. Thank you. Next slide, please. So what I have
done in this slide is to place the graphic summaries of the
argument from irreducible complexity that I just made in the
upper left-hand corner of the slide, and in the upper right-hand
corner, I have basically put the evolutionary explanation using
the same graphic convention. And the nature of the test that I or
any other scientist would propose is pretty simple.

If you animate the slide, you'll see that Dr.
Behe's prediction is that the parts of any irreducibly complex
system should have no useful function. Therefore, we ought to be
able to take the bacterial flagellum, for example, break its
parts down, and discover that none of the parts are good for
anything except when we're all assembled in a flagellum.

If evolutionary theory holds, however, and we can
animate again, and we'll show that in the right-hand side,
evolution makes an extremely straight forward prediction. And
that is, when we look at these irreducibly complex structures, we
ought to be able to find parts of those systems that actually do
have useful functions within them.

So we can do a very straight forward either/or
test to distinguish between these two alternatives. So what I'd
like to show in the next slide is how such a test can be
conducted. This is a -- in the upper right-hand corner of the
slide is a graphic representation from a review article showing
some of the proteins involved in the construction of the
bacterial flagellum.

Now the individual names of the gene products need
not concern us. They often begin with FL for flagellum. But as
you can see, just as Dr. Behe says, this is a complex multi-part
biochemical machine. Now the test that I would propose, we can
animate the slide, please, to start with this flagellum. And if
Dr. Behe is correct, if we take away even one part, there should
be no function.

But I'm going to propose that we take away not
one, not two, I'm going to propose we take away 30 parts. And
what I'm going to propose to do is, take 30 of these proteins
away and see what is left. And the slide that I set up is
animated, and what we have done is -- actually, could you go back
for the animation and then do it again?

And let's watch the Court do it, and we'll do the
animation now. Thank you. And you can see the parts that I have
removed are on the outside and the inside, and what are left are
10 proteins that span the inner and outer membrane. These
bacteria, many of them are surrounded by two membranes.

These 10 remaining parts are shown in the next
diagram, which will come up on the slide. And this is a diagram
showing where these 10 parts are. They exist at the very base of
the flagellum near one of the cellular membranes.

Now the prediction that is made by Dr. Behe in his
book is extremely straight forward, which is, since this was an
irreducibly complex machine, and we've taken away most of its
parts, what's left behind should be non-functional because, you
remember, he wrote, any pre-cursor to an irreducibly complex
machine that is missing a part is, by definition, non-functional.
This guy is missing 30 parts.

Next slide. Well, it turns out that what is
actually left behind when we take those parts away is a little
structure with those 10 parts, which is known to microbiologists
as the type III secretory system. And I can see, Mr. Walczak,
you're saying, why, of course, it's the type III secretory
system.

THE WITNESS: Exactly. Now I was expecting a
question of, how do you know it's not type II or type IV? The
type III secretory system is a little molecular syringe that some
of the nastiest bacteria in all of nature have. Yrsinia pestis,
for example, which is the organism that causes bubonic plague, is
a type III secretor. And what it does is, it gets inside our
body, crawls up alongside, and uses this syringe to inject
poisons into a human cell.

And in the lower left-hand corner of the slide, I
have some diagrams showing the operation of a type III secretory
system. Now the connection between this and the flagellum is that
the type III -- the 10 proteins in the type III system are almost
a precise match for the corresponding 10 proteins in the base of
the bacterial flagellum.

So it's very clear that a subset of those proteins
has an entirely different function, a beneficial function, not
for us, but for the bacterium, and a function that can and is
favored by natural selection. Can I have the next slide, please?
So the summary of this example is really very straight
forward.

When we take this complex multi-part system, which
is the bacterial flagellum, the prediction made by Dr. Behe from
irreducible complexity is when we break the parts apart, we
should have no useful functions. Anyone missing a part is, by
definition, non-functional. We follow that up. We do break it
apart. And lo and behold, we find -- actually, we find a variety
of useful functions, one of which I have just pointed out, which
is type III secretion.

What that means, in ordinary scientific terms is
that, the argument that Dr. Behe is made is falsified, it's
wrong, it's time to go back to the drawing board.

Q. And does Dr. Behe focus on just one type of
cell? I'm sorry if I'm using the wrong terms here.

A. No, he doesn't. His arguments extend to a wide
variety of cells and a wide variety of systems that he identifies
as irreducibly complex.

Q. But the reasoning, the analysis that you just
went through is -- applies in the same fashion to these other
examples, is that correct?

A. Yes, it would. And if I could redirect the
Court's recollection to earlier today, one of those systems was,
in fact, the blood clotting cascade. And Pandas, and as it turns
out, Dr. Behe's book, Darwin's Black Box, makes the same
statement, which is that, all of the parts have to be together
for blood to clot effectively.

The exact quotation, I think, is, if even one part
is missing, the system fails and blood does not clot. And I then
showed that when we look for, for example, at the genome sequence
of the puffer fish, we find that three of the parts are missing
and blood still clots perfectly well.

That is exactly the same kind of argument, which
we just examined, and also found wanting in another of Dr. Behe's
chosen examples, which is the flagellum.

Q. I asked you, in preparation, to select a third
example, and that was the immune system. What is the immune
system?

A detailed look at Behe's claims that the immune system could not have
evolved.

A. Well, it's a very good question, because we all
depend for our very lives on a functioning immune system. It's a
system of our body that is widely distributed. We have cells from
our immune system sort of engaging in patrol, floating throughout
the blood stream and the tissues. And it's a system that enables
us to identify, defend against, and to repel foreign
invaders.

When I was a little boy, for example, it was on
vacation, too, which I never really liked very much, I got the
chicken pox, and I was very, very sick. And it was during spring
vacation, so I had the wonderful experience of being sick during
vacation week. But chicken pox is a virus when invades the human
body, the immune system recognizes the code proteins on the
virus, makes cells that can continue to recognize it, and
produces proteins called antibodies that will bind to the surface
of the virus.

What that meant is, once I had gone through that
miserable week with the chicken pox, I could be confident I would
never get it again. I would be permanently immune to the chicken
box. This is a very important realization for medicine to have
because, of course, most of us in this room have received
vaccinations designed to stimulate our immunity from diseases far
worse than chicken pox such as, for example, polio and diptheria
and whooping cough in an effort to stipulate our immune systems
to make sure we never get sick from those diseases.

Q. Have you prepared a presentation on the immune
system that will help you to explain this?

A. Yes, sir, I have. And if we could show the
first slide, I want to start -- and, Your Honor, I may have to
stand up to --

THE WITNESS: Thanks. I thought I would start by
pointing out an essential protein of the immune system. You can't
work without it. That essential protein is sometimes -- it is
called by researchers an immunoglobulin, but it is more commonly
called an antibody. These are the essential molecules of the
immune system.

In the upper left-hand corner of the slide, there
is a molecular diagram for what an antibody actually looks like.
It basically is a little Y shaped molecule with two binding
sites. And you'll notice in the slide, those binding sites are
labeled foreign particle binding sites. I hope I have antibodies
circulating in my bloodstream against chicken pox. So if I get
chicken pox virus in my body, that foreign particle binding site
on my chicken pox antibody will bind to the surface of the virus.
Another one will bind to the other site.

And gradually, the virus will be cross linked into
a mesh world, which my immune system recognizes, eliminates from
the circulation, and destroys. And that's why, hopefully, I'm not
going to get chicken pox again. Now in the lower right-hand is a
more diagrammatic view of this molecule. It's made up of four
parts.

These are each polypeptides, and they're
diagrammed. And you'll notice that part of these -- each of the
polypeptides is colored blue, and another part is colored red.
The red says, variable region. Now I know some of my own
vaccination history, so I've been vaccinated against polio,
diptheria, measles, and a number of other diseases.

The antibodies in my body against polio differ
from the antibodies I have against diptheria in the variable
regions. They have a different shape because the viruses or the
bacteria have different molecules on the surface.

The genius, if you will, of the immune system, is
that it can produce an antibody that will attach to, stick to,
identify, and destroy just about anything. So one of the most
important things in our immune system is the ability, basically,
to produce antibodies against any conceivable molecule that might
get inside our body. Can I have the next slide?

Now about 20 years ago, a scientist working at MIT
named Susumu Tonegawa -- I know I'm going to have to spell that
for the court reporter -- determined exactly how antibodies had
the ability to produce such diversity. And that is, it turns out
to be a system in the genes of cells in the immune system known
as a VDJ recombination system.

And this system is not at all unlike a dealer
shuffling a deck of cards, and that at a certain point in
development, parts of DNA, in a variety of genes, are literally
shuffled. They're tossed from one side to another, and they are
rearranged to form a final gene. Now some elements of this
shuffling are random just like you hope the dealer, when you go
to Las Vegas, is shuffling those card randomly so you don't know
what you're going to get.

But it's in that random shuffling that our immune
system develops the ability to produce an antibody to just about
anything. That shuffling is at the heart of why the immune system
works. If anything goes wrong with this process, the individual
in which it goes wrong loses the ability to make diverse
antibodies, they get very sick, and they're in big trouble when
they start to see foreign organisms.

Now the next slide. Where did this system come
from? That's the question that people interested in evolution
always try to answer. About 10 years ago, a number of scientists,
including Nobel Prize winner David Baltimore, speculated that
this process, which is called VDJ recombination, might actually
have evolved from a system known as transposition, a system in
which genes jump around.

What I have placed on the slide in addition to
this diagram and the reference to the
Baltimore group's paper in
the
Proceedings of the National Academy of Sciences is a
quotation from this paper illustrating his hypothesis. They, and
he means the gene shuffling system, could have been part of
retrotransposons and had a DNA rearrangement function this their
previous life. It's possible that the ancestors of these genes,
they're called RAG genes, may have been horizontally transferred
into a metazoan multi-cellular animal lineage at a recent point
in evolution.

So he argued, he suggests there might be an
evolutionary way to explain where this system came from. It's a
very interesting suggestion. And as I wrote in the slide, perhaps
the three part system arose from a type of mobile genetic element
known as a transposon. It's a hypothesis, but the important
point, and the reason it's useful is that, it is a testable
hypothesis.

Can I have the next slide, please? Now Dr. Behe
was aware when he wrote Darwin's Black Box of the speculations of
the Baltimore lab.

Q. So Dr. Behe addressed that. And he regarded
this as mere speculation. And he also basically told researchers,
don't bother. And the reason you shouldn't bother is actually
given in the bottom of the slide. On page 130 of Darwin's Black
Box, he wrote, and I quote, In the absence of the machine --
that's the gene shuffling machine -- the parts never get cut and
joined.

In the absence of the signals for where to cut,
it's like expecting the machine that's randomly cutting paper to
make a paper doll. And, of course, in an absence of the message
for the antibody itself, the other components would be useless,
closed quote. So he basically argues, because this is a
multi-part system and all parts had to be together for it to work
ahead of time, you're not going make any progress.

A few pages later, he's even more explicit about
that. On page 139, he wrote, quote, As scientists, we yearn to
understand how this magnificent mechanism came to be, but the
complexity of the system dooms all Darwinian explanations to
frustration.
Sisyphus himself would pity us. I hope you're up on
your classical mythology.

A. What's happened since then is, I think, very
interesting. Can I have the next slide? This is the quote from
Dr. Behe. The complexity of the system dooms all Darwinian
explanations to frustration. If you animate the slide,
please.

In 1996, the same year that Darwin's Black Box
came out, very strong biochemical similarities were found between
this shuffling process, the VDJ recombination, and the way in
which retroviruses shuffle their DNA, very suggestive.

A. The -- well, the
report is in the journal
Science. This particular case, I believe, was found in a
prokaryotic system because retroviruses can go into all sorts of
systems. But the important point is, these investigators noticed
there were biochemical similarities between the way the genes are
shuffled in the immune system and the way that retroviruses go
into other cells.

A. Happy to.
Two years later in the journal
Nature, which I have plugged repeatedly as a great publication,
it turns out that the cutting and transposing enzymes that are
normally used for these transposable genetic elements can be
replaced by the RAG enzymes, which do the cutting and pasting in
the immune system. So that's suggested a further biochemical
similarity between these two systems published in 1998 in the
journal Nature. Also, of course, peer reviewed. Can I have the
next element, please?

In 2000, the RAG enzymes were shown to cause
transposition in mammalian cells. What this meant was, not only
can they shuffle the immune system pieces of DNA, they can
shuffle other pieces of DNA as well. So little by little, we're
beginning to understand that elements of the Baltimore hypothesis
are being born out by published research in peer review
journals.

A. Blood is also a peer reviewed journal. This is
an original research paper subjected to the usual process of
review. Can I have the next slide, please? Once again, the quote
that we've been talking about, if you could advance it, in 2003,
the VDJ recombinase was shown to cause transposition -- in other
words, shuffle DNA around -- not just in mammalian cells, but in
human cells as well.

The next animation, please, will show the
transposases were discovered in nature not associated with the
immune system that are a perfect mimic for the way the immune
system gene shuffling machine works in human cells. And this was
in the journal Nature.

And finally, the last part of this puzzle was put
together in the last year, and that is the actual transposic from
which these enzymes and insertion sequences evolved were
identified by a
paper printed in the Public Library of Science,
which is a brand new, but very highly regarded peer review
journal, and this is
Kapitonov & Jurka in 2005.

It's worth noting how these researchers described
their own work. And the next slide will show a facsimile of the
paper, and also has a quotation from the abstract. Now this is
absolutely filled with technically latent language, but it shows
how thoroughly researchers have explored this particular -- this
particular hypothesis.

And what I will do is, I will read, and I'm going
to skip parts of this, but I'm going to read, starting at the
quotation marks, and I will skip over some of the technical
terminology. Quote, The significant similarity between the
transib transpases and RAG core, the common structure of these
transpases and others, as well as the similar size of these
basically catalyzed by these enzymes directly support the
25-year-old hypothesis of a transposon related origin of the VDJ
machinery.

And the researchers then point out, there have
been other hypotheses that have been considered. Previously, the
RAG transposon hypothesis was open to challenge by alternative
models of convergent evolution. Because there were no known
transpases similar to the gene shuffling ones, the RAG ones
found, it could be argued that our gene shuffling enzymes, the
RAG1 independently developed some transposon-like properties
rather than deriving them from a transposable element encoded
transpases. These arguments can now be put to rest.

And they're very straight forward about saying, we
have solved the puzzle of where this system came from. It came
from evolution. And it came from a transposable element system.
Can I have the next slide, please? Okay.

So the summary of what we have just gone through,
and this is a tree analysis of these transposons and humans and
mammals are right down where it says, mammals, is that the
summary is that between 1996 and 2005, each element of the
transposon hypothesis has been confirmed and, furthermore, when
the enzymes that do this gene shuffling are actually put to an
analysis to see how closely related they are to see if they
themselves match the evolutionary predicted tree, they match that
tree perfectly. So we've got it.

Q. So what do you tell your mother about what all
this means for Dr. Behe's theory?

THE WITNESS: I was about to say, my mother and
Your Honor, but Your Honor, not being a retired nurse like my
mother, my mother is deeply interested in immunity. And I often
remind her that the reason I got chicken pox in the first place
is because she wanted me to have immunity to it, so she marched
me down the street to play with Denny Marsh who had chicken pox
at the time to make sure that I would get sick. And she forgot to
realize that 10 days later, which is the incubation period, was
going to be spring break for me, spring vacation for me.

Your Honor, I've never forgiven my mother for that
to this day. So we'll have to take that up. So the important
point basically is that, we have, in our immune system, as an
essential part of our survival, the ability to shuffle genetic
information so as to make it possible for our immune cells to
make an antibody to just about anything.

That shuffling ability was proposed 10 years ago
to have evolved from sequences known as transposable genetic
elements. In 10 years of research, every step of that hypothesis
has been confirmed. And we, therefore, do know, as the result of
investigation using evolutionary theory, where that came from and
how this gene shuffling ability arose. It also means -- could we
advance to the next slide, please? Actually, I'm sorry, I forgot
that. I'm finished with the slides. It also means that the
prediction that Dr. Behe quite confidently made on the basis of
intelligent design theory, that this system would not be amenable
to Darwinian investigation, that there would be no evolutionary
explanation for it, turned out to be wrong, and I am happy to say
that fortunately research scientists did not listen to him.

If they had listened to him, they might not have
done this research, and we might not have had this fundamental
breakthrough in how the immune system works.

Q. Did Dr. Behe, in fact, rely on this argument,
that the immune system could never be explained by natural
selection to argue that, in fact, there must be an intelligent
designer?

A. Yes, sir, he did. And this is actually one of
several arguments that he raises in Darwin's Black Box to say
that, if you cannot, in principle, explain the origin of a
complex system by evolutionary means, that is by invoking the
negative, that is evidence for an intelligent designer. This is
another essential example in his list of irreducibly complex
systems.

Q. Let me direct your attention now to Plaintiff's
Exhibit 665. And not to be redundant, but, in fact, is there now
even more research on the immune system that has come out even
this past week?

A. Well, yes, it has. And as I was getting ready
to pack up and come to Harrisburg for this trial, I happened to
glance over the Internet at the latest issue of the journal
Nature, which has actually not yet appeared in print. I'm still
waiting for my copy in the mail. But fortunately, you can on look
at things on the Internet several days ahead of time.

The VDJ recombination system is not the only
important part of the immune system. There is another important
part known as the
compliment system. And in this case, compliment
does not mean, say something nice about somebody. Compliment in
this case is a system that compliments or completes part of
what's known as the immune response.

And it consists of a series of proteins that
target and destroy. And they destroy, in a molecular sense in a
most vicious way possible, foreign invaders, especially bacteria
and foreign cells. One of the key elements of this is a
compliment component now as C.. this article reported, and this
is from Jansen et al. It's from a combined Dutch and Scandinavian
group. And again, it's in the latest issue of Nature.

They, for the first time, worked out the detailed
structure of compliment C.. and the structure of compliment C.
Immediately told them how this compound must -- how this protein
must have evolved. It was made up of a series of modular units of
exactly the sort that one would expect to arise by gene
duplication, and the molecule had unmistakable sites in which
pieces of another gene became recombined with it to produce the
complete molecule. Hence, they title this work
structures of
compliment component C. Provide insights into the function and
evolution of immunity.

So the entire idea of evolutionary theory is
providing a fruitful avenue of investigation into every aspect of
the immune system, not just the gene shuffling that I've talked
about, but into this other area known as compliment.

Q. I'm listening to the arguments that you have
described Dr. Behe is making, that these components are
irreducibly complex, and that science cannot explain them. And in
some cases, he's been shown wrong. But is that essentially the
argument, that scientists currently can't explain some aspects of
evolution?

A. In essence, that is the argument. It is what a
philosopher might call the argument from ignorance, which is to
say that, because we don't understand something, we assume we
never will, and therefore we can invoke a cause outside of
nature, a supernatural creator or supernatural designer.

Q. And is this not a completely negative argument?
I mean, it sounds like this is an attack on evolution?

A. This is in every respect a completely negative
argument. And if one combs the pages Of Pandas and People or, for
that matter, if one looks at Dr. Behe's book or if one looks at
the writings of other people who consider themselves to be
intelligent design advocates, all that one finds is example after
example, argument after argument, as to why evolution couldn't
produce this, didn't make that, and doesn't provide an
explanation for the following.

I have yet to see any explanation, advanced by any
adherent of design that basically says, we have found positive
evidence for design. The evidence is always negative, and it
basically says, if evolution is incorrect, the answer must be
design. Never considers an alternative idea.

Q. Now let me just stop you. Just because science
today cannot explain something, does that mean it can never be
explained?

A. Of course not. And if it did, no one would do
scientific research. What attracts scientists to research is the
lure of the unknown. There is nothing more dreadful than to wake
up one morning and think that all the fundamental problems in
your field has been solved. On the day that I think all
fundamental problems in cell biology have been resolved, I will
retired to Sussex and keep bees, as Sherlock Holmes once
said.

You want unsolved problems. You're attracted to
them. I'll just give you a very simple example. Proteins are
built by hooking together strings of amino acid, almost like
beads on a string. The machine that does that building is called
a ribosome. We have worked for years to understand the detailed
molecular structure of the ribosome.

As a result of work that's been published in the
last couple years, we know the internal structure of the ribosome
down to the atomic level. We can now look inside it, and we can
see the molecular details of how these two amino acids are
brought into very close proximity.

But do you know what? There's still an unsolved
problem. We still don't understand the chemistry that forges the
link between those two beads on a chain. There was a very popular
hypothesis that was put forward by Peter Moore at Yale
University. But in the last year, a number of experimenters,
including Al Dahlberg at my own university, has shown that
Moore's ideas are wrong.

So what scientists everywhere realize is, there's
a great prize to be won. That's very exciting. To find the
mechanism by which these are joined together. What no one is
doing is to say, we'll never solve it, we're going to attribute
the formation of the bond between amino acids to an unseen
outside force operating beyond nature and, therefore, any
chemical explanation is doomed to failure.

That's something we never say in science, because
if we did, it would be a research stopper. It would tell us, give
up, go home, we'll never figure it out.

Q. What is Dr. Behe's argument? What evidence does
Dr. Behe, and -- well, strike that. Dr. Behe's argument is
consistent with the arguments made in Pandas, I believe you
testified before?

A. Yes, sir, that's exactly what I testified. The
term irreducible complexity, which is a feature of Dr. Behe's
book, does not appear in Pandas. But the core idea behind
irreducible complexity, which is in these complex systems, all
parts must be assembled in order to have function, that is at the
heart and soul of the arguments which are in Pandas.

Q. Now what I've heard are these negative
arguments about evolution. What is the evidence in Pandas? Let's
start with Pandas. What is the affirmative evidence for a
designer?

A. I'm not aware that there is any affirmative
evidence for a designer anywhere in that book.

A. As far as I can tell, there is no affirmative
evidence for a designer in Dr. Behe's book either. Both books
rely entirely on negative inferences by saying that, if evolution
has problems, if evolution is wrong, if evolution cannot provide
complete explanations, then we can go ahead and say it's a
designer.

Q. So how do they make that argument? I mean, even
if there's no evidence? What's the rationale? What's the
reasoning for getting to that designer?

A. Well, with all due respect, I believe I've
already answered that question, which is, I don't find there is
any reasoning in that area at all. It's the sort of logical
fallacy in which you might say, well, I have theory A, and I have
theory B. And I can prove theory B by showing theory A is wrong.
And in science, you say, excuse me, just a minute.

Besides theory B, there's an infinite number of
other possible theories. So you don't, quote, prove one by
showing that another one is wrong. If you show another one is
wrong, you've shown that it's wrong. All other alternative
theories are now equal contenders. So the logic of picking out
intelligent design, which is inherently untestable, and saying
that any evidence against evolution is evidence for intelligent
design employs a logical fallacy that I think most scientists
reject.

Q. So the argument is that, if science can't
explain it, that default is, a designer?

A. That is the argument, as I understand it, and
as it is expressed in both of these books.

Q. Has the scientific community taken a position
similar to yours about intelligent design not being science?

A. Well, the scientific community, of course, is
large and diverse, and I'm sure there are a few people who are
enamored of intelligent design. As I mentioned earlier, the
largest scientific organization in the United States, the one
organization that probably can fairly be said to speak on behalf
of the scientific community in this country is the
American
Association for the Advancement of Science, or AAAS. I know they
have indeed taken a position on this issue.

A. Yes, sir, I do. This is a board resolution by
the governing board of AAAS on intelligent design theory.

Q. If we can highlight the passages. And Dr.
Miller, could you read the highlighted text?

A. I'd be glad to. Quote, Whereas ID, intelligent
design, proponents claim that contemporary evolutionary theory is
incapable of explaining the origin of diversity of living
organisms, whereas to date, the ID movement has failed to offer
credible scientific evidence to support their claim that ID
undermines the current scientifically accepted theory of
evolution, wheres as the ID movement has not proposed a
scientific means of testing its claim, therefore, be it resolved
that the lack of scientific warrant for so-called intelligent
design theory makes it improper to include it as a part of
science education, closed quote.

A. Quote, Creationism, intelligent design, and
other claims of supernatural intervention in the origin of life
or of species are not science because they are not testable by
the methods of science. These claims subordinate observed data to
statements based on the authority, revelation, or religious
belief. Documentation offered in support of these claims is
typically limited to the special publications of their
advocates.

These publications do not offer hypotheses subject
to change in light of new data, new interpretations, or
demonstration of error. This contrasts with science where any
hypothesis or theory always remains subject to the possibility of
rejection or modification in the light of new knowledge, close
quote.

Q. Are you aware of any scientific organizations
that have taken a position that intelligent design is
science?

A. I am not aware of any scientific organization
that has taken a position that intelligent design is science, not
one.

Q. Why do you believe that intelligent design, as
described in Pandas and by Professor Behe, is a form of, I think
as you put, special creationism?

A. I believe that as a proper analysis for the
following reason. Each of the systems described by Dr. Behe had
their origination, their first appearance at some time in the
natural history of this planet. Each of the organisms described
in Pandas and People and said to appear suddenly, fully formed in
the fossil record had their origin at a particular time in the
past. To say that such organisms are designed or such pathways
are designed is only to tell part of the story.

Because, for example, if the blood clotting
cascade had only been designed, our blood wouldn't clot. That
pathway had -- that design had to be executed. It had to be
created. It had to be put into physical form. And by any
definition, that is an act of creative energy and power.

What that means, for example, the bacterial
flagellum perhaps originated a billion years ago. It means the
first organism containing that flagellum had to be created. The
blood clotting cascade came into existence, we think, about 450
million years ago. The genes, the co-factors, the pathways had to
be created. Advocates of intelligent design point to the first
appearance of many major animal groups in what is known as the
Cambrian period of geologic history.

If one says that those organisms were designed,
they also had to be created. So that the natural history of this
planet, according to intelligent design advocates, is marked by
instance after instance after instance of specific and special
creation. Saying that something is designed, as I mentioned, is
only part of the story. We won't know about the design unless
somebody created it and put it into execution, and that is what
makes intelligent design inherently a theory of special
creation.

Q. Now does intelligent design differ from
creation science or scientific creationism what you are debating
in the early 1980's?

A. In the early 1980's, the scientific creationist
movement proposed a number of essential tenants or doctorates.
One of them was that, the earth is about 6 to 10,000 years old.
Another one is that, all of the geological column of this planet
was formed in a single world wide flood, so that geologists are
wrong when they talk about ages in the past; in fact, everything
was laid down in about 40 days and 40 nights, that humans and
apes have separate ancestory, that biochemical and biological
systems show evidence of design, and that the mechanism of
evolution does not work.

These are all elements, as I understand them, of
the creation science or the creationist or scientific creationism
movement. Now the difference between this movement and
intelligent design ironically is that intelligent design has
withdrawn the testable scientific predictions made by scientific
creationists.

The statement that the earth is only 6000 years
old is a testable scientific statement. They've withdrawn that.
The statement that all of the geological formations of this
planet were laid down in a 40 day, 40 night flood, that's
actually a testable statement. They've withdrawn from that.

The only thing that they have left is an
untestable assertion, and that assertion is that the living
things on this planet are too complex to have been explained by
evolution and, therefore, they must be the work of a supernatural
designer creator working outside of the laws of nature
unidentifiable and not subject to detection, analysis, or
identification.

So, as I said, ironically, intelligent design is
somewhat less scientific in terms of the prediction it makes than
scientific creationism, but it shares that core belief, and that
is that design can be attributed to a supernatural designer or
creator.

Q. I want to switch gears now and bring us back
from the classroom, so to speak, to the classroom at Dover,
Pennsylvania. I'd like to direct your attention to Plaintiff's
Exhibit 124. Again, this is the four paragraph statement that was
read to the students in January of 2005.

You indicated earlier that you did not -- you
believed that this statement did not promote students'
understanding of evolution in particular or science and biology
generally. I'm wondering if you could comment a little bit more
specifically about your views on this four paragraph statement.
And perhaps we want to take it paragraph at a time?

A. Yeah, I was going to -- thank you very much. I
was simply going to ask for the whole statement to be put up
there. I'd be happy to discuss this statement with you in a
number of ways. We could parcel it word by word and line by line,
if you had the patience to do that.

But I think it's probably better to take it first
a paragraph at a time and basically see what it says. Well, that
first paragraph basically says, kids, we have to teach evolution
whether we want to or not because the State of Pennsylvania
requires us to.

The second paragraph says, oh, by the way, we
don't really believe this stuff, it's a theory not a fact. There
are gaps. There's no evidence. We're very skeptical of this.

The third paragraph said, by the way, there's
another alternative really good idea called intelligent design,
and we're going to provide you with curricular material and the
book Pandas and People so you can explore it. And I say that
because I note that, there's no statement in here that
intelligent design is theory not a fact, that it has gaps which
cannot be explained. Those are only pointed out for
evolution.

The third paragraph says, basically we think this
is a pretty good theory, and we're giving it our endorsement. The
fourth one basically reminds students basically, go home, discuss
this with your families, and reminds them again, oh, by the way,
we have to test you on this stuff whether we want to or not
because the State of Pennsylvania requires us to.

Now when I read this, and I try to think of how a
student will react to this, what it basically tells students who
have studied theory after theory and subject after subject and
hypothesis after hypothesis in earth science, in physical
science, in chemistry and biology, it says, oh, by the way, of
all the stuff you studied, we want to warn you about just one of
those things. And that one thing is evolution. We have to teach
evolution whether we like it or not. We think it's pretty
shaky.

There is this other theory called intelligent
design which we think is on a very sound footing. Go home, talk
it over with mom and dad, and, oh, yeah, remember, we have to
test you on evolution.

Q. Dr. Miller, I'd like to focus your attention
back onto the second paragraph. And this makes various assertions
about evolution generally. And maybe we could go through that
sentence by sentence.

A. Okay. I'd be glad to do that. The first
sentence reads, quote, Because Darwin's theory is a theory, it
continues to be tested as new evidence is discovered, closed
quote. Well, it certainly is true that the theory of evolution is
a theory. That's almost redundant. That's obvious from the
terminology.

It continues to be tested. All scientific theories
are continued to be tested. So to pick out evolution and say, by
the way, it's a theory, and we're going to keep testing it,
implies to students that really this is the only theory that we
have to continue to keep testing. Other theories, they're fine.
They're on sound footing. But this one, we have to keep working
on.

Q. I'm sorry. From your textbook, evolution is not
the only theory that is presented for 9th grade biology?

A. Of course not. And we talk about cell theory
and the germ theory of disease. We even talk about the pressure
flow hypothesis of phloem transfer. I've never seen a statement
in the textbook saying, keep your eye on that special pressure
flow hypothesis in phloem transfer.

This is the only theory people seem to be
concerned about. The Dover statement, first of all, basically
begins in this paragraph by calling special attention to just one
part of the curriculum, and that is evolution.

Now the second sentence, the theory is not a fact.
As far as that reads, that's actually a true statement. No
scientific theory is a fact. That's not because we're sure of
facts and we're not certain about theories. It's because theory
is a higher level of scientific understanding than fact. Theories
explain facts.

And if this statement said, no scientific theory
is a fact, but rather, theories are based on facts and supported
by facts, and theories explain facts, it would be fine. But by
saying, the theory is not a fact, it essentially invites students
to say, you know what, other theories might be factual, this one
isn't. And that implication is incorrect.

The next sentence reads, gaps in the theory exist
for which there is no evidence. I continue -- I have to tell you,
I have read that statement hundreds of times, and I don't
understand what it means by gaps in the theory. There certainly
are elements in the natural history of our planet for which
evidence is missing. There are pieces of our natural history that
we don't know, just like there are pieces of our political,
military, and human history that we don't know.

I can only trace one part of my family back to
about 1850. I don't know what happened before that. That doesn't
mean I couldn't possibly be here because I don't have any
ancestors before 1850. It means, I don't have the whole story.
Well, that's true about evolution as well. There are parts of our
recent past that are gaps, that are missing, that we don't have
the story.

But to say that's a gap in the theory strikes me
as very very strange. There are missing pieces of evidence but
not gaps in the theory. And then the last sentence, a theory is
defined as a well-tested explanation that unifies a broad range
of observations. Do you know what? That's fine.

And if evolutionary theory had been introduced in
this paragraph by saying, evolutionary theory is a well-tested
explanation for the origin of life that unifies -- for the origin
of species that unifies a broad range of observations, I'd be
saying, terrific, that's a very useful thing to tell
students.

Q. As an author of a textbook, biology textbook
for high school students, does this promote sound scienc
education?

A. No, I certainly don't think it does. I think
it, in fact, undermines sound scientific education in a number of
ways. First of all, it misleads students into the relationship
between theory and fact. Secondly, it undermines the scientific
status of evolution in a way that it does to no other scientific
theory as if to pretend to students, we are certain of everything
we're going to teach in biology this year except for
evolution.

And that certainly gives students a false
understanding of evolution. And I think, as an experimental cell
biologist, it gives them a false certainty of the rest of
science, which is equally damaging. And then finally, to say that
there are gaps for which there are no evidence, once again, is
targeting evolution for a very specific purpose, and that is to
create doubt and confusion in the minds of students about the
scientific status of evolution and evolutionary theory.

Q. The School District argues, you know, it takes
a minute to read this statement. I haven't timed it. It takes
about a minute to read this statement. What's the big deal?
What's the harm in reading this to Dover School District
students?

A. That's a very interesting point. And if they
raised the issue, what is the harm in reading it, one might well
turn around and say, well then why read it in the first place, if
it makes so little difference, if it is of so little consequence?
Then why have you insisted on doing this and why are you in court
today?

The only thing I can infer from turning that
question around is that the Dover School Board must think this is
enormously important to compose this, to instruct administrators
to read it, to be willing to fight all the way to the court. They
must think that this performs a very important function.

Now turning it around back to my side of the
table, do I think this is important? You bet I think this is
important for a couple of reasons. One of which, first of all, as
I mentioned earlier, it falsely undermines the scientific status
of evolutionary theory and gives students a false understanding
of what theory actually means. Now that's damaging enough.

The second thing is, it is really the first
attempt or the first movement to try to drive a wedge between
students and the practice of science, because what this really
tells students is, you know what, you can't trust the scientific
process. You can't trust scientists. They're pushing this theory.
And there are gaps in the theory. It's on shaky evidence. You
really can't believe them. You should be enormously
skeptical.

What that tells students basically is, science is
not to be relied upon and certainly not the kind of profession
that you might like to go into. And thirdly, that third paragraph
that we haven't talked about very much right now points out that
intelligent design, which has implicit endorsement in this
statement, because we don't hear that it's just a theory, we
don't hear that it's being tested, it sounds like it's a pretty
good explanation. It's available. It's good stuff. And students
will understand immediately, as anybody does who reads Pandas,
that the argument is made on virtually every page of Pandas for
the existence of a supernatural creator designer.

And by holding this up as an alternative to
evolution, students will get the message in a flash. And the
message is, over here, kids. You got your God consistent theory,
your theistic theory, your Bible friendly theory, and over on the
other side, you got your atheist theory, which is evolution. It
produces a false duality. And it tells students basically, and
this statement tells them, I think, quite explicitly, choose God
on the side of intelligent design or choose atheism on the side
of science.

What it does is to provide religious conflict into
every science classroom in Dover High School. And I think that
kind of religious conflict is very dangerous. I say that as a
person of faith who was blessed with two daughters, who raised
both of my daughters in the church, and had they been given an
education in which they were explicitly or implicitly forced to
choose between God and science, I would have been furious,
because I want my children to keep their religious faith.

I also want my students to love, understand,
respect, and appreciate science. And I'm very proud of the fact
that one of my daughters has actually gone on to become a
scientist. So by promoting this, I think, this is a tremendously
dangerous statement in terms of its educational effect, in terms
of its religious effect, and in terms of impeding the educational
process in the classrooms in Dover.

THE COURT: I was going to break about 3:00, Mr.
Walczak. Is that good for you. If you want to move onto another
line of questioning, this might be a good time to do it.

MR. ROTHSCHILD: I'm done, Your Honor. I would just
move the exhibits into evidence.

THE COURT: Is there an objection, first of all, to
any of the exhibits?

THE COURT: We'll get those in the record when we
come back from the break. I think we have a list. Why don't you
compare notes with Liz and make sure that we've got a
comprehensive roster of the exhibits. We'll take at least a 20
minute break or so. So my friends in the jury box who look like
they could use a little caffeine, this will give you ample time
to patronize the local establishments and get some caffeine and
come back. That not a knock on you, Doctor.